This repository is for development of ITS1-based diagnostic/profiling tools for the THAPBI Phyto-Threats project, funded by BBSRC.
In this repository, we're trying to keep to the Python PEP8 style convention, the PEP257 docstring conventions, and the Zen of Python. To help in this, a pre-commit hook script is provided in the git_hooks subdirectory that, if deployed in the Git repository, checks Python code for PEP8 correctness before permitting a git commit command to go to completion.
If the pep8 module is not already present, it can be installed using pip install pep8
Whether you choose to use this or not, the THAPBI-pycits repository is registered with landscape.io, and the "health" of the code is assessed and reported for every repository push.
To install the pre-commit hook:
- clone the repository with
git clone https://github.com/widdowquinn/THAPBI(you may already have done this) - change directory to the root of the repository with
cd THAPBI-pycits - copy the pre-commit script to the
.git/hooksdirectory withcp git_hooks/pre-commit .git/hooks/
In the root directory of the repository:
$ virtualenv -p python3.5 venv-THAPBI-pycits
$ source venv-THAPBI-pycits/bin/activate
<activity>
$ deactivate
All Python module dependencies are described in requirements.txt and can be installed using
pip install -r requirements.txt
There may be issues with biom-format and biopython installations due to ordering of module installation. If this is the case for you, then it might be solved by installing numpy at the command-line first, with:
pip install numpy
pip install -r requirements.txt
pear is a paired-end read merger, used by the pipeline to merge ITS paired-end reads into a single ITS sequence. It is available from the pear home page as a precompiled executable that can be placed in your $PATH, and it can be installed on the Mac with Homebrew and homebrew-science, using:
If you are having trouble on some Linux system due to bzip+zlib issues, a precompiled version is availble: https://github.com/xflouris/PEAR/blob/master/bin/pear-0.9.5-bin-64
brew install pear
please rename the binary to pear:
wget http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.10-bin-64.tar.gz
tar -zxvf pear-0.9.10-bin-64.tar.gz
cp pear-0.9.10-bin-64/pear-0.9.10-bin-64 pear-0.9.10-bin-64/pear
put this in your PATH
Trimmomatic is used to trim and quality-control the input reads. pycits expects Trimmomatic to be available at the command-line as trimmomatic. You can check if the tool is installed this way with the command:
which trimmomatic
To obtain Trimmomatic with this installation type on Linux systems, you can use:
apt-get install trimmomatic
and on the Mac (with Homebrew and homebrew-science):
brew install trimmomatic
If you have downloaded the Java .jar. file from trimmomatic's home page, you can wrap the .jar file with a Bash script called trimmomatic in your $PATH, such as
#!/bin/bash
exec java -jar $TRIMMOMATIC "$@"
where $TRIMMOMATIC is the path to your trimmomatic .jar file.
muscle MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences [muscle download page]http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz as a precompiled executable that can be placed in your $PATH when decompressed. Please rename to muscle
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz
tar -zxvf muscle3.8.31_i86linux32.tar.gz
cp muscle3.8.31_i86linux32 muscle
put this in your PATH
fastqc fastqc A quality control tool for high throughput sequence data. [fastqc download page]http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux32.tar.gz as a precompiled executable that can be placed in your $PATH when decompressed.
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
unzip fastqc_v0.11.5.zip
cd FastQC
chmod 755 fastqc
put this in your PATH
spades spades is an assembly program which we use for error correction. [spades download page]http://spades.bioinf.spbau.ru/release3.9.1/SPAdes-3.9.1-Linux.tar.gz as a precompiled executable that can be placed in your $PATH when decompressed.
wget http://spades.bioinf.spbau.ru/release3.9.1/SPAdes-3.9.1-Linux.tar.gz
tar -zxvf SPAdes-3.9.1-Linux.tar.gz
cd ./SPAdes-3.9.1-Linux/bin/
put this in your PATH
flash flash is a pair end read assembly program. [flash download page]https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz as a precompiled executable that can be placed in your $PATH when decompressed.
wget https://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz
tar -zxvf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
put this in your PATH
swarm swarm is a clustering program. [swarm download page]https://github.com/torognes/swarm
git clone https://github.com/torognes/swarm.git
cd swarm/src
make
put PATH_TO/swarm/bin in your PATH
blastclust blastclust is a clustering program. This is not essential to download. [blastclust download page]ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz as a precompiled executable that can be placed in your $PATH when decompressed.
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy/2.2.26/blast-2.2.26-x64-linux.tar.gz
tar -zxvf blast-2.2.26-x64-linux.tar.gz
put this in your PATH
cd-hit cd-hit is a clustering program. [cd-hit download page]https://github.com/weizhongli/cdhit
git clone git@github.com:weizhongli/cdhit.git
cd cdhit
make
put PATH_TO/cdhit in your PATH
bowtie_2.2.5 bowtie_2.2.5 is a read mapping program. [bowtie_2.2.5 download page]https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz
We have use the pre compiled binary to reduce difficulty in getting this to work.
mkdir bowtie_2.2.5
cd bowtie_2.2.5
wget https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz
tar -zxvf bowtie2-2.2.5-Linux-x86_64.tar.gz
put this in your path
export PATH=$HOME/bowtie_2.2.5/bin/:$PATH
samtools_1.2 samtools_1.2 is a program to do lots of thing with sam/ bam files. [samtools_1.2 download page]https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz
We have use the pre compiled binary to reduce difficulty in getting this to work.
mkdir samtools_1.2
cd samtools_1.2
wget https://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz
tar -zxvf samtools-1.2-Linux-x86_64.tgz
put this in your path
export PATH=$HOME/samtools_1.2/bin/:$PATH
vsearch vsearch Versatile open-source tool for metagenomics. [vsearch download page]https://github.com/torognes/vsearch
wget https://github.com/torognes/vsearch/releases/download/v2.4.0/vsearch-2.4.0-linux-x86_64.tar.gz
tar xzf vsearch-2.4.0-linux-x86_64.tar.gz
- Git hooks (
git): https://git-scm.com/book/en/v2/Customizing-Git-Git-Hooks - Git hooks (tutorial): http://githooks.com/
- PEP8: https://www.python.org/dev/peps/pep-0008/
- PEP257: https://www.python.org/dev/peps/pep-0257/
- Zen of Python (PEP20): https://www.python.org/dev/peps/pep-0020/